High power density is one of the competitive edges of proton exchange membrane fuel cell (PEMFC), making it a promising technology for many applications. However, its intensive heat generation leads to a high cooling burden, and a large amount of low-grade waste heat is difficult to utilize, which brings technical difficulty to the system's thermal management. In this study, the organic fluid (R245fa) with low boiling temperature is selected for the PEMFC stack's phase change cooling, and the organic Rankine cycle (ORC) is employed to recover waste heat. Four cooling channels are designed: serpentine straight, spiral straight, serpentine thin and serpentine zigzag channels. The boiling flow is simulated to reveal the effect of channel layout, sectional size and channel shape on the cooling and heat recovery performance. The results show that the cooling plates can be cooled to a reasonable temperature by the organic fluid, and the maximum surface temperature difference is within 15 K, which demonstrates the good cooling performance of flow boiling. The highest ORC thermal efficiency of 7% is achieved by the serpentine straight channel and the spiral straight channel, while the serpentine zigzag channel has the best temperature uniformity contribution resulting from its secondary circulation flow. This study demonstrates the potential of flow boiling on PEMFC thermal management and gives guidance on the cooling channel design.